Environmental microbiology !
CLS416!
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Lecture 1!
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Fundamentals of microbial ecology!
Sarah Alharbi
outline!
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1)
2)
3)
4)
microbial ecology & environmental microbiology!
ecosystem!
Physical environment, Niche and biofilms!
ecological role of microorganisms
Microbial Ecology Vs Environmental Microbiology
- “Microbial ecology is the study of the behavior and activities of
microorganisms in their natural environments.!
- “microbes are small; their environments also are small.” In these
small environments or “microenvironments,” other kinds of
microorganisms (and macroorganisms) often also are present,.!
Thomas D. Brock,
Environmental microbiology, relates to all-over microbial processes that occur in a soil, water, or food, It
is not concerned with the particular “microenvironment” where the microorganisms actually are functioning,
but with the broader-scale effects of microbial presence and activities.
Ecosystem
- Ecosystems have been defined as “communities of organisms and their physical and chemical
environments that function as self-regulating units.” These self-regulating biological units
respond to environmental changes by modifying their structure and function.
- It includes a wide range of biological, physical, and chemical processes that connect organisms and
their environment.
Figure.1 Levels of ecological organization
Components of ecosystem
1)Abiotic components!
!
include the non-living or physico-chemical factors like air, soil, water and the basic
compounds and elements of the environment!
!
2) Biotic components!
It consists of the living parts of the environment, including the association of a lot of
interrelated populations that belong to different species inhabiting a common
environment.
Prescott−Harley−Klein:
Microbiology, Fifth Edition
Physical environment
!
!
- Microorganisms, as they interact with each other and
with other organisms in biogeochemical cycling, are
influenced by their immediate physical environment
whether this might be soil, water, the deep marine
environment, or a plant or animal host.!
620
Chapter 28
VIII. Ecology and
Symbiosis
28. M
Intera
Ecolo
Microorganism Interactions and Microbial Ecology
Particle
Aerobic
region
!
Microorganism
Anaerobic
region with
sulfide
Particle
- Microenvironment: the specific physical location of
a microorganism.!
!
- Niche,includes the microorganism, its physical
habitat, the time of resource use, and the resources
available for microbial growth and function!
!
!
!
!
Oxygen
concentration
Sulfide
concentration
Specialized
niche
for aerobic sulfideoxidizing microorganisms
Figure 28.26
The Creation
a Niche
from
Microenvironment.
Figure2.
The Creation
of a of
Niche
from
a aMicroenvironment.!
As shown in this illustration, two nearby particles create a physical
microenvironment for possible use by microorganisms. Chemical
gradients, as with oxygen from the aerobic region, and sulfide from the
anaerobic region, create a unique niche. This niche thus is the physical
environment and the resources available for use by specialized aerobic
sulfide-oxidizing bacteria.
Biofilms
Klein:
h Edition
VIII. Ecology and
28. Microorganism
© The McGraw−Hill
Microorganisms
tend
to create their own microenvironments
and niches, even without having a
Symbiosis
Interactions and Microbial
Companies, 2002
structured
physical
environment
available,
by
creating
biofilms.!
Ecology
Biofilms are organized microbial systems consisting of layers of microbial cells associated with
surfaces!
nism Interactions and Microbial Ecology
e
sm
Anaerobic
region with
sulfide
(a)
Sulfide
concentration
(b)
e
Specialized
niche
aerobic sulfideg microorganisms
of a Niche from a Microenvironment.
wo nearby particles create a physical
use by microorganisms. Chemical
the aerobic region, and sulfide from the
ue niche. This niche thus is the physical
available for use by specialized aerobic
(c)
Figure 28.27 The
Growth
of Biofilms.
Biofilms, or microbial
Figure.3.
The
growth
of biofilms.
a)Initial colonization by a single type of bacterium.b)
growths on surfaces
such as
in freshwater
andwith
marine
environments,
Development
of a more
complex
biofilm
layered
microorganisms of different types. c)A mature biofilm with cell
can
develop
and
become
extremely
complex,
depending
on
the
energy
aggregates, interstitial pores, and conduits.
Prescott−Harley−Klein:
Microbiology, Fifth Edition
VIII. Ecology and
Symbiosis
Biofilms
28. Microorganism
Interactions and Microbial
Ecology
© The McGraw−Hill
Companies, 2002
28.4
- Protect pathogens from disinfectants,
create a focus for later occurrence of
disease, or release microorganisms
and microbial products that may affect
the immunological system of a
susceptible host.
Inert surfaces
Dirty food bowl
Trickling filter unit
!
For example:!
!
- Air-conditioning and other water
retention systems where potentially
pathogenic bacteria, such as
Legionella species, may be
protected from the effects of
chlorination by biofilms
!
- Teeth, where biofilm forms plaque
that leads to tooth decay
!
- Contact lenses, where bacteria may
produce severe eye irritation,
inflammation, and infection
!
The Physical Environment
A contact lens
A catheter device
Rocks in a stream
Used syringe
Living organism surfaces
Teeth and gum region
The tongue
Urinary tract tissue surface
Skin
Figure 28.28 Biofilm Formation on Inert and Living Organism Surfaces. Biofilms, noted in yellow, are a
part of microbial functioning in the environment, in biotechnology, and in human health.
figure.4, Biofilm Formation on living and nonliving surfaces
disease, or release microorganisms and microbial products that
may affect the immunological system of a susceptible host.
Biofilms are critical in ocular diseases because Chlamydia, Staphylococcus, and other pathogens survive in ocular devices such as
contact lenses and in cleaning solutions (figure 28.29).
Depending on environmental conditions, biofilms can become so large that they are visible and have macroscopic dimensions. Bands of microorganisms of different colors are evident as
shown in figure 28.30. These thick biofilms, called microbial
mats, are found in many freshwater and marine environments.
These mats are complex layered microbial communities that can
form at the surface of rocks or sediments in hypersaline and
freshwater lakes, lagoons, hot springs, and beach areas. They
consist of microbial filaments, including cyanobacteria. A major
characteristic of mats is the extreme gradients that are present.
Light only penetrates approximately 1 mm into these communi-
621
Prescott−Harley−Klein:
Microbiology, Fifth Edition
VIII. Ecology and
Symbiosis
Ecological role of microorganisms
Microorganisms in ecosystems can have two
complementary roles: (1) the synthesis of new
organic matter from CO2 and other inorganic
compounds during primary production and
(2) de- composition of this accumulated
organic matter.!
- primary producers, decomposers, and
primary consumers.!
CO2
Tertiary-level consumers
CO2
Secondary-level consumers
Primary consumers
Carbon
fluxes
CO2
Bacteria and fungi
OM
28. Microorgan
Interactions an
Ecology
CO2 (Chemoheterotrophs)
OM
Primary producers
(Photoautotrophs,
chemoautotrophs)
Figure 28.32 The Vital Role of Microorganisms in Ecosystems.
Microorganisms play vital roles in ecosystems as primary producers,
decomposers, and primary consumers. Carbon is fixed by the primary
producers, including microorganisms, which use light or chemically
bound energy. Chemoheterotrophic bacteria and fungi serve as the
main decomposers of organic matter, making minerals again available
for use by the primary producers. Ciliates and flagellates, important
microbial primary consumers, feed on the bacteria and fungi, recycling
nutrients as part of the microbial loop. Organic matter (OM).
what are the important effects of microbial groups in nature
Ecological role
Primary producers
Secondary producers, assimilating
dissolved organic matter
Principal Microbial groups involved
photoautotrophs ( microalagae&photosynthetic bacteria)
Chemoautotrophs( bacteria& archaea)
!
Bacteria, archaea,fungi,protozoa
a food source for consumers
Microalgae, cyanobacteria, bacteria,archaea, protozoa
important links between producers
and top consumers
protozoa
Decomposing organic matter
Bacteria, archaea, fungi
biogeochemical cycling
All
structuring communities
Viruses, Bacteria
Soil formation
Fungi, bacteria
Thank you